neurom.io.utils¶

Utility functions and for loading neurons.

Functions

`get_files_by_path`	Get a file or set of files from a file path.
`get_morph_files`	Get a list of all morphology files in a directory.
`load_data`	Unpack data into a raw data wrapper.
`load_neuron`	Build section trees from an h5 or swc file.
`load_neurons`	Create a population object.

Classes

`DataWrapper`	Class holding a raw data block and section information.
`FstNeuron`	Class representing a neuron.
`NeuronLoader`	Caching morphology loader.
`Population`	Neuron Population Class.

Exceptions

`NeuroMError`	Base class for all NeuroM exceptions.
`RawDataError`	Exception class for raw data errors.

class neurom.io.utils.DataWrapper(data_block, fmt, sections=None)[source]¶

Bases: object

Class holding a raw data block and section information.

neurite_root_section_ids()[source]¶: Get the section IDs of the intitial neurite sections.

soma_points()[source]¶: Get the soma points.

class neurom.io.utils.FstNeuron(data_wrapper, name='Neuron')[source]¶

Bases: neurom.core._neuron.Neuron

Class representing a neuron.

transform(trans)[source]¶: Return a copy of this neuron with a 3D transformation applied.

exception neurom.io.utils.NeuroMError[source]¶

Bases: Exception

Base class for all NeuroM exceptions.

class neurom.io.utils.NeuronLoader(directory, file_ext=None, cache_size=None)[source]¶

Bases: object

Caching morphology loader.

Parameters

directory – path to directory with morphology files
file_ext – file extension to look for (if not set, will pick any of .swc|.h5|.asc)
cache_size – size of LRU cache (if not set, no caching done)

get(name)[source]¶: Get name morphology data.

class neurom.io.utils.Population(neurons, name='Population')[source]¶

Bases: object

Neuron Population Class.

Features:

flattened collection of neurites.
collection of somas, neurons.
iterable-like iteration over neurons.

exception neurom.io.utils.RawDataError[source]¶

Bases: neurom.exceptions.NeuroMError

Exception class for raw data errors.

neurom.io.utils.get_files_by_path(path)[source]¶

Get a file or set of files from a file path.

Return list of files with path

neurom.io.utils.get_morph_files(directory)[source]¶

Get a list of all morphology files in a directory.

Returns: list with all files with extensions ‘.swc’ , ‘h5’ or ‘.asc’ (case insensitive)

neurom.io.utils.load_data(handle, reader=None)[source]¶: Unpack data into a raw data wrapper.

neurom.io.utils.load_neuron(handle, reader=None)[source]¶: Build section trees from an h5 or swc file.

neurom.io.utils.load_neurons(neurons, neuron_loader=<function load_neuron>, name=None, population_class=<class 'neurom.core.population.Population'>, ignored_exceptions=())[source]¶

Create a population object.

From all morphologies in a directory of from morphologies in a list of file names.

Parameters

neurons – directory path or list of neuron file paths
neuron_loader – function taking a filename and returning a neuron
population_class – class representing populations
name (str) – optional name of population. By default ‘Population’ or filepath basename depending on whether neurons is list or directory path respectively.

Returns

neuron population object